<html><head></head><body dir="auto" style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div dir="auto" style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div class="ApplePlainTextBody">Mirco,<br><br>on the modification - nicely done.<br>On the system speed, running Maestro-Desmond one core ) the 1080ti is pegged and at usually 90% power. them folks at Schrodinger know what they are doing. So the base speed is apparently sufficient, its some other factor e.g. the work load distribution that is not optimized.<br><br>I’ll work with your files tomorrow and let you know how it turns out— thanks <br><br>Have a a great weekend<br><br>Paul<br><br><blockquote type="cite">On Jan 12, 2019, at 3:11 PM, Wahab Mirco <Mirco.Wahab@chemie.tu-freiberg.de> wrote:<br><br>Hi Paul,<br><br>thanks for your reply.<br><br>On 11.01.2019 23:20, paul buscemi wrote:<br><blockquote type="cite">Getting the ion and SOL concentration correct in the top is trickier ( for me ) than it should have been, If you happen to reuse both solvate and genion during the build keeping track of the top is like using a digital rubics cube..! The charge the villin was +1 because after I downloaded it from the pdb I removed all other water and ions - it just made pdb2gmx easier to work with.<br><br></blockquote><br>I simply hand-edited the .gro by making up two ions and put them<br>somewhere near the corners and added a short energy minimization.<br>Then, I added one line in the .top for the ions.<br><br><blockquote type="cite">The 1080 scaled nicely with the 1080 ti, these are really nice pieces of hardware. and you are correct, given the choice of increased processors vs faster processors - choose the latter. I have the AMD OC to 4.0 GH and it runs the same model almost as fast as as 32 core AMD at 3.7 GHz.<br></blockquote><br>Your system is possibly too slow to saturate the 1080Ti at this small<br>system size. In a much larger system, the lead of the 1080 Ti over the<br>1080 may possibly reach the theoretical expectation.<br><br><blockquote type="cite">I've run 300k DPPC models ( ~300 DPPC molecules ) and they run at ~15 ns/day in NPT. And yes, if you can send the pdb, top, and itps I’t would be interesting to compare the two AMDs.<br><br></blockquote><br>I did upload the stuff here + a readme-file. This system is much too<br>large for a single box + GPU (for productive runs), but maybe in 5 years<br>or so we can watch capillary waves through connected IMD/VMD in real-<br>time ;)<br><br>=> http://suwos.gibtsfei.net/d.dppc.4096.zip<br><br>Regards<br><br>Mirco<br><br>-- <br>Gromacs Users mailing list<br><br>* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!<br><br>* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br><br>* For (un)subscribe requests visit<br>https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request@gromacs.org.<br></blockquote><br></div></div></body></html>